Extract DNA from a GTO¶
p3-gto-dna.pl [options] gtoFile
This script reads one or more locations from the standard input and outputs the corresponding DNA from the input GenomeTypeObject file.
The positional parameter should be the name of the GenomeTypeObject file in JSON format.
The standard input can be overridden using the options in Input Options. The standard input should contain location
strings in the key column (specified using Column Options) and the region name in the column identified by the
Location strings are of the form contigID
+len for the forward strand and contigID
the backward strand.
Additional command-line options are as follows.
Output should be in FASTA format, with the region name as the ID.
Index (1-based) or name of the column containing the region names. The default is the first column (